TALgetter - Revision history

Grau: /* Running the command line application */

2017-01-25T19:58:04Z

Running the command line application

← Older revision		Revision as of 19:58, 25 January 2017
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	<tr>		<tr>
	<td><font color="green">strand</font></td>		<td><font color="green">strand</font></td>
	<td>Both strands (Search both strands of the input sequence for target sites, default = false)</td>		<td>Both strands (Search both strands of the input sequence for target sites, default = false) [since v1.1, default value restores previous behaviour]</td>
	<td>Boolean</td>		<td>Boolean</td>
	</tr>		</tr>

Grau: /* Running the command line application */

2017-01-25T19:57:24Z

Running the command line application

← Older revision		Revision as of 19:57, 25 January 2017
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	<td>Training data (The input data to use for training the model, annotated FastA, OPTIONAL)</td>		<td>Training data (The input data to use for training the model, annotated FastA, OPTIONAL)</td>
	<td>String</td>		<td>String</td>
			</tr>
			<tr>
			<td><font color="green">strand</font></td>
			<td>Both strands (Search both strands of the input sequence for target sites, default = false)</td>
			<td>Boolean</td>
	</tr>		</tr>
	</table>		</table>

Grau at 12:00, 1 September 2013

2013-09-01T12:00:08Z

← Older revision		Revision as of 12:00, 1 September 2013
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	If you use TALgetter, please cite		If you use TALgetter, please cite

	J. Grau, A. Wolf, M. Reschke, U. Bonas, S. Posch, and J. Boch. [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002962 Computational predictions provide insights into the biology of TAL effector target sites]. ''PLOS Computational Biology'', 2013.		J. Grau, A. Wolf, M. Reschke, U. Bonas, S. Posch, and J. Boch. [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002962 Computational predictions provide insights into the biology of TAL effector target sites]. ''PLOS Computational Biology'' 9 (3), 2013.

	== TALgetter web-server ==		== TALgetter web-server ==

Grau at 11:48, 1 September 2013

2013-09-01T11:48:07Z

← Older revision		Revision as of 11:48, 1 September 2013
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	In addition, we provide the [http://www.jstacs.de/download.php?which=TALgetterWeb Jar of the Galaxy web-application] for installing it in your local [http://getgalaxy.org Galaxy] server.		In addition, we provide the [http://www.jstacs.de/download.php?which=TALgetterWeb Jar of the Galaxy web-application] for installing it in your local [http://getgalaxy.org Galaxy] server.

	TALgetter ~~will be~~ part ~~of the next public~~ release of the ~~Jstacs library. Meanwhile, we provide all source files of~~ TALgetter ~~and required additional and modified~~ sources ~~of Jstacs [http://www~~.~~jstacs.de~~/~~download.php?which=TALgetter-src as a separate download]. As (future) part of Jstacs, TALgetter is released under GPL 3~~.		TALgetter is part if Jstacs release 2.1. You find the TALgetter sources in package <code>projects.tals</code>.

	== Running the command line application ==		== Running the command line application ==

Grau at 19:21, 29 May 2013

2013-05-29T19:21:52Z

← Older revision		Revision as of 19:21, 29 May 2013
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	by Jan Grau, Annett Wolf, Stefan Posch and Jens Boch.		by Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch and Jens Boch.

	TALgetter allows you to scan input DNA sequences for putative target sites of a given TAL (transcription activator like) effector as typically expressed by many ''Xanthomonas'' bacteria.		TALgetter allows you to scan input DNA sequences for putative target sites of a given TAL (transcription activator like) effector as typically expressed by many ''Xanthomonas'' bacteria.

Grau: /* Paper */

2013-03-26T11:36:33Z

Paper

← Older revision		Revision as of 11:36, 26 March 2013
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	If you use TALgetter, please cite		If you use TALgetter, please cite

	[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002962 ~~J. Grau, A. Wolf, M. Reschke, U. Bonas, S. Posch, and J. Boch.~~ Computational predictions provide insights into the biology of TAL effector target sites. 'PLOS Computational Biology', 2013.]		J. Grau, A. Wolf, M. Reschke, U. Bonas, S. Posch, and J. Boch. [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002962 Computational predictions provide insights into the biology of TAL effector target sites]. ''PLOS Computational Biology'', 2013.

	== TALgetter web-server ==		== TALgetter web-server ==

Grau: /* Paper */

2013-03-26T11:35:24Z

Paper

← Older revision		Revision as of 11:35, 26 March 2013
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	If you use TALgetter, please cite		If you use TALgetter, please cite

	[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002962 J. Grau, A. Wolf, M. Reschke, U. Bonas, S. Posch, and J. Boch. Computational predictions provide insights into the biology of TAL effector target sites. PLOS Computational Biology, 2013.]		[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002962 J. Grau, A. Wolf, M. Reschke, U. Bonas, S. Posch, and J. Boch. Computational predictions provide insights into the biology of TAL effector target sites. 'PLOS Computational Biology', 2013.]

	== TALgetter web-server ==		== TALgetter web-server ==

Grau at 11:35, 26 March 2013

2013-03-26T11:35:04Z

← Older revision		Revision as of 11:35, 26 March 2013
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	We provide TALgetter as a public web-server, a web-application that can be installed in a local Galaxy server, and as a command line program.		We provide TALgetter as a public web-server, a web-application that can be installed in a local Galaxy server, and as a command line program.

			== Paper ==
			If you use TALgetter, please cite

			[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002962 J. Grau, A. Wolf, M. Reschke, U. Bonas, S. Posch, and J. Boch. Computational predictions provide insights into the biology of TAL effector target sites. PLOS Computational Biology, 2013.]

	== TALgetter web-server ==		== TALgetter web-server ==

Grau at 15:42, 18 March 2013

2013-03-18T15:42:14Z

← Older revision		Revision as of 15:42, 18 March 2013
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	After the training, the estimated parameters are printed to STDERR and the predictions are printed to STDOUT, and you can redirect these to different files.		After the training, the estimated parameters are printed to STDERR and the predictions are printed to STDOUT, and you can redirect these to different files.

			== Large input data sets ==

			Currently, TALgetter is restricted to at most 90 Mb due to memory requirements for computing empirical p-values. As an alternative, you can [http://www.jstacs.de/download.php?which=TALgetterLong download] a version of TALgetter with limited options (especially computation of p-values is disabled) for scanning large input data sets (e.g., complete genomes).

	== Installing the web-application ==		== Installing the web-application ==

Grau: /* Download */

2012-12-11T19:32:19Z

Download

← Older revision		Revision as of 19:32, 11 December 2012
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	TALgetter is implemented in Java using Jstacs. You can download the command line application as a [http://www.jstacs.de/download.php?which=TALgetter Jar].		TALgetter is implemented in Java using Jstacs. You can download the command line application as a [http://www.jstacs.de/download.php?which=TALgetter Jar].
	In addition, we provide the [http://www.jstacs.de/download.php?which=TALgetterWeb Jar of the Galaxy web-application] for installing it in your local [http://getgalaxy.org Galaxy] server.		In addition, we provide the [http://www.jstacs.de/download.php?which=TALgetterWeb Jar of the Galaxy web-application] for installing it in your local [http://getgalaxy.org Galaxy] server.

			TALgetter will be part of the next public release of the Jstacs library. Meanwhile, we provide all source files of TALgetter and required additional and modified sources of Jstacs [http://www.jstacs.de/download.php?which=TALgetter-src as a separate download]. As (future) part of Jstacs, TALgetter is released under GPL 3.

	== Running the command line application ==		== Running the command line application ==